Fix tree topology and branch lengths to initial tree.

[Nicola de maio]

Hi all,

I want to run BEAST on simulated data using the simulated tree as fixed, and estimating only the rates.
Now, I specify the initial tree with:

    <rescaledTree id="startingTree">
        <newick usingDates="false">
            ((4:0.143716199312,3:0.143716199312):906.962270176,(2:1.33042015929,1:1.33042015929):905.775566216);
        </newick>
    </rescaledTree>

As created by Beauti, and I remove all operators on branch lengths and topology.
This successfully results in the topology being fixed to the one of the initial tree.
Branch lengths are also fixed, but not to the right values, in fact I get in the tree log file:

tree STATE_0 [&lnP=-19.028510823779968,posterior=-19.028510823779968] = [&R] ((4:2.0,3:2.0):1.0,(2:2.0,1:2.0):1.0);

etc..
Changing the sequence alignment does not alter the branch lengths.
How can I rather fix branch lengths to the ones in the input tree?

Thanks,
Nicola

[Andrew Rambaut]

Dear Nicola,

Try changing this:

<rescaledTree id="startingTree">
<newick usingDates="false">
((4:0.143716199312,3:0.143716199312):906.962270176,(2:1.33042015929,1:1.33042015929):905.775566216);
</newick>
</rescaledTree>

to this:

<newick id="startingTree" usingDates="false">

((4:0.143716199312,3:0.143716199312):906.962270176,(2:1.33042015929,1:1.33042015929):905.775566216);
</newick>

Best,
Andrew

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[Nicola de maio]

Many thanks, it works perfectly!

Nicola

[Luis]

Hi there,

I have one question about adding a starting tree. I already assigned node ages and prior densities of certain clades of a tree using beauti. I want to add a starting (and fix) tree in the xml file; do I need to incorporate the node ages to this starting tree before running beast?

Cheers

L